I admit to not spending a whole lot of time wondering whether or not she's 'ready'. It simply seemed obvious to me that, as of Seasons 5 and 6, she is and has been being groomed (by Jack and by the writers) as a future team leader. Because of RDA's lessened role, and also because of the way stories have gone, Sam has found herself in leadership roles far more significant than her little foray in "Spirits". In "The Sentinel", she had the responsibility of keeping the Jaffa away long enough for the others to get the machine working, and ultimately wound up in the position of making a life of death choice. (Ah, forcefields. You gotta love em!) Threaded throughout recent seasons have been cases, such as "Shadowplay", where she's taken more of a 'spokesperson' role than she previously has. "Paradise Lost" demonstrated that Sam is part of what I'm sure is a very short list to command SG-1, should anything happen to Jack. (This could be contrasted with "Shades of Gray", where she and Hammond decided what someone else (specifically someone of higher rank) should head the team. Or you could say that this doesn't count because it was all part of the plan. I guess it depends whether or not they suspected Makepeace from the beginning at all. Anyway.)
As well as establishing this changing attitude towards Sam militarily, there have been changes to the character that I think are also noteworthy. She's a lot more relaxed now, a lot more comfortable in her own skin than she was at the beginning of the series (which can be attributed to AT becoming more comfortable, I know, but stay with me here). Some have pointed out that her arguing with Jack (such as in "Unnatural Selection") is a sign that she's unprofessional... at the very least insubordinate. But with a role model like Jack (King of Insubordination ;)), what else do you expect? As Sam grows, she gets more experience on the field, gets her own ideas about how things should be done, starts changing from a follower into a leader in her own right. (That's why I liked Hailey -- even if she was incredibly annoying, she allowed a different side of Sam to emerge -- the "I outrank you and don't you forget it" side. As a Major, she does outrank a lot of people, but seeing as how the show is focused on SG-1, she doesn't interact with enlisted on a regular basis). Two strong differences of opinion are going to clash; that's part of the reason people go all ga-ga over Jack and Daniel. Initially Sam was far more restrained in her disagreement; she had to be. But now, she has more leeway, more pull with 'the boys' than she had in the early seasons. And she knows it.
Whew. That's a lot of thinking. I'll continue later.